OMERO.web installation separately from OMERO.server on Debian 9 and IcePy 3.6

Please first read OMERO.server installation on Debian 9.

This is an example walkthrough for installing OMERO.web decoupled from the OMERO.server in a virtual environment using OMERO.py and a dedicated system user. Installing OMERO.web in a virtual environment is the preferred way. For convenience in this walkthrough, we will use the omero system user and define the main OMERO.web configuration options as environment variables.

The following steps are run as root.

If required, first create a local system user omero and create the homedir too /home/omero:

useradd -m omero

chmod a+X /home/omero

Installing prerequisites

The following steps are run as root.

Install ZeroC IcePy 3.6. IcePy is managed by PyPI, a package management system used to install and manage software packages written in Python. IcePy and will be installed as part of the OMERO.web requirements:

# to be installed if recommended/suggested is false
apt-get -y install build-essential python-dev

apt-get -y install libssl-dev libbz2-dev libmcpp-dev libdb++-dev libdb-dev libdb-java

Install other dependencies. The number of dependencies to install depends on the way you plan to install OMERO.web. If you wish to install it in a virtual environment created with --system-site-packages on (option 1), you will need to install python-pillow and python-numpy. If you wish to install it in a virtual environment with --system-site-packages off, a few more dependencies will be required (option 2):

# dependencies common to both options
apt-get update

apt-get -y install unzip

apt-get -y install python-pip python-virtualenv

# to be installed if recommended/suggested is false
apt-get -y install virtualenv

apt-get -y install nginx

# To install OMERO.web using option 1
apt-get -y install python-pillow python-numpy

# To install OMERO.web using option 2
# require to install Pillow
apt-get -y install libtiff5-dev libjpeg8-dev zlib1g-dev
apt-get -y install libfreetype6-dev liblcms2-dev libwebp-dev
apt-get -y install tcl8.6-dev tk8.6-dev

Creating a virtual environment

The following steps are run as the omero system user.

Create the virtual environment. This is the preferred way to install OMERO.web:

# option 1: in a virtual environment with --system-site-packages on
virtualenv /home/omero/omerowebvenv --system-site-packages

# option 2: in a virtual environment with --system-site-packages off
virtualenv /home/omero/omerowebvenv

Installing OMERO.web

The following steps are run as the omero system user.

Install OMERO.web using OMERO.py:

cd /home/omero
curl -o OMERO.py.zip -L https://downloads.openmicroscopy.org/latest/omero5/py.zip
unzip -q OMERO.py*

zip=$(ls OMERO.py*.zip)
rm -f $zip
ln -s OMERO.py-* OMERO.py

The following steps are run as the omero system user.

Install the OMERO.web requirements. Select one of the commands corresponding to the way you have opted to install it:

# option 1: in a virtual environment with --system-site-packages on
/home/omero/omerowebvenv/bin/pip install --upgrade -r /home/omero/OMERO.py/share/web/requirements-py27.txt

# option 2: in a virtual environment with --system-site-packages off
/home/omero/omerowebvenv/bin/pip install --upgrade -r /home/omero/OMERO.py/share/web/requirements-py27-all.txt

Installing OMERO.web apps

The following steps are run as the omero system user.

A number of apps are available to add functionality to OMERO.web, such as OMERO.figure and OMERO.iviewer. See the main website for a list of released apps. These apps are optional and can be installed via pip to your OMERO.web virtual environment at any time.

Configuring OMERO.web

The following steps are run as the omero system user.

For convenience the main OMERO.web configuration options have been defined as environment variables. You can either use your own values, or alternatively use the following ones:

export WEBPORT=80
export WEBSERVER_NAME=localhost

Configure OMERO.web and create the NGINX OMERO configuration file:

. /home/omero/omerowebvenv/bin/activate

/home/omero/OMERO.py/bin/omero config set omero.web.application_server wsgi-tcp
/home/omero/OMERO.py/bin/omero web config nginx --http "${WEBPORT}" --servername "${WEBSERVER_NAME}" > /home/omero/nginx.conf.tmp

For more customization, please read Customizing your OMERO.web installation.

Configuring Gunicorn

The following steps are run as the omero system user.

Additional settings can be configured by changing the following properties:

Configuring NGINX

The following steps are run as root.

Copy the generated configuration file into the NGINX configuration directory, disable the default configuration and start NGINX:

sed -i.bak -re 's/( default_server.*)/; #\1/' /etc/nginx/nginx.conf
mv /etc/nginx/sites-available/default /etc/nginx/sites-available/default.disabled
if [ -f /etc/nginx/sites-enabled/default ]; then
    rm /etc/nginx/sites-enabled/default
fi
cp /home/omero/nginx.conf.tmp /etc/nginx/conf.d/omeroweb.conf

service nginx start

Running OMERO.web

The following steps are run as the omero system user.

Install WhiteNoise:

. /home/omero/omerowebvenv/bin/activate

pip install --upgrade 'whitenoise<4'

Configure WhiteNoise and start OMERO.web manually to test the installation:

. /home/omero/omerowebvenv/bin/activate

/home/omero/OMERO.py/bin/omero config append -- omero.web.middleware '{"index": 0, "class": "whitenoise.middleware.WhiteNoiseMiddleware"}'

/home/omero/OMERO.py/bin/omero web start

# Test installation e.g. curl -sL localhost:4080

/home/omero/OMERO.py/bin/omero web stop

Automatically running OMERO.web

The following steps are run as root.

Should you wish to run OMERO.web automatically, a init.d file could be created. See below an example file omero-web-init.d:

#!/bin/bash
#
# /etc/init.d/omero-web
# Subsystem file for "omero" web
#
### BEGIN INIT INFO
# Provides:             omero-web
# Required-Start:       $local_fs $remote_fs $network $time omero postgresql
# Required-Stop:        $local_fs $remote_fs $network $time omero postgresql
# Default-Start:        2 3 4 5
# Default-Stop:         0 1 6
# Short-Description:    OMERO.web
### END INIT INFO
#
### Redhat
# chkconfig: - 98 02
# description: init file for OMERO.web
###

RETVAL=0
prog=omero-web

# Read configuration variable file if it is present
[ -r /etc/default/$prog ] && . /etc/default/$prog


OMERO_PY=${OMERO_PY:-/home/omero/OMERO.py}
OMERO_USER=${OMERO_USER:-omero}
OMERO=${OMERO_PY}/bin/omero
VENVDIR=${VENVDIR:-/home/omero/omerowebvenv}

start() {
    echo -n $"Starting $prog:"
    su - ${OMERO_USER} -c ". ${VENVDIR}/bin/activate; ${OMERO} web start" &> /dev/null && echo -n ' OMERO.web'
    sleep 5
    RETVAL=$?
    [ "$RETVAL" = 0 ]
        echo
}

stop() {
    echo -n $"Stopping $prog:"
    su - ${OMERO_USER} -c ". ${VENVDIR}/bin/activate; ${OMERO} web stop" &> /dev/null && echo -n ' OMERO.web'
    RETVAL=$?
    [ "$RETVAL" = 0 ]
        echo
}

status() {
    echo -n $"Status $prog:"
    su - ${OMERO_USER} -c ". ${VENVDIR}/bin/activate; ${OMERO} web status"
    RETVAL=$?
}

case "$1" in
    start)
        start
        ;;
    stop)
        stop
        ;;
    restart)
        stop
        start
        ;;
    status)
        status
        ;;
    *)
        echo $"Usage: $0 {start|stop|restart|status}"
        RETVAL=1
esac
exit $RETVAL

Copy the init.d file, then configure the service:

cp omero-web-init.d /etc/init.d/omero-web
chmod a+x /etc/init.d/omero-web

update-rc.d -f omero-web remove
update-rc.d -f omero-web defaults 98 02

Start up services:

cron
service nginx start
service omero-web restart

Maintenance

The following steps are run as the omero system user.

Please read OMERO.web maintenance.